|
| Status |
Public on Jul 18, 2022 |
| Title |
H3K27me3_GM12878 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: rabbit anti H3K27me3 (Active Motif 39055)
|
| Treatment protocol |
isolated nuceli were treated for DiMeLo-seq with conditions described above
|
| Growth protocol |
Cells grown in RPMI-1640 with 15% FBS, 1% penn/strep at 37C with 5% CO2
Human cells grown in RPMI with 15% FBS, 1% penn/strep at 37C with 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NEB Monarch genomic DNA extraction kit (T3010S)
Oxford Nanopore sequencing libraries were generated with SQK-LSK110
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
Megalodon (v2.3.1), Guppy (v4.5.4), using a Rerio res_dna_r941_min_modbases-all-context_v001.cfg basecalling model
fast5s were aligned and modified bases were called using Megalodon (2.3.1 or 2.3.4) using the rerio all-context basecalling model (res_dna_r941_min_modbases-all-context_v001.cfg) with parameters --outputs mod_mappings and --mod-min-prob 0
Assembly: CHM13v1.1 reference genome or dm6
Supplementary files format and content: bam files with alignment and modification basecalling info
Library strategy: DiMeLo-seq
|
| |
|
| Submission date |
Jul 13, 2022 |
| Last update date |
Jul 18, 2022 |
| Contact name |
Aaron Streets |
| E-mail(s) |
astreets@berkeley.edu
|
| Organization name |
University of California, Berkeley
|
| Department |
Bioengineering
|
| Street address |
Stanley Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE208125 |
Protocol for Mapping Protein-DNA Interactions with Directed Methylation with Long-read Sequecing (DiMeLo-seq) |
|
| Relations |
| BioSample |
SAMN29486230 |
| SRA |
SRX16028823 |
